I'm assuming his diet consists of other foods that would trigger a reaction if this were the case. Unless he's eating oatmeal and juicing and the only hard food he eats is almonds. Even then I would think you would notice if it were chewing related.
Possibly an allergen on the almond, not the almond itself. Not all almonds are distributed through the same company.
Nuts can have all sorts of stuff on them organic or not. Sprout your own almonds and try that. Then report back.